Isolation and identification of a bacterium with high tolerance to lead and copper from a marine microbial mat in Spain

Screening of Native Trichoderma Species for Nickel and Copper Bioremediation Potential Determined by FTIR and XRF

Soil pollution with heavy metals is a serious threat to the environment. However, soils polluted with heavy metals are considered good sources of native metal-resistant Trichoderma strains. Trichoderma spp. are free-living fungi commonly isolated from different ecosystems, establishing endophytic associations with plants. They have important ecological and biotechnological roles due to their production of a wide range of secondary metabolites, thus regulating plant growth and development or inducing resistance to plant pathogens. In this work we used indigenous Trichoderma strains that were previously isolated from different soil types to determine their tolerance to increased copper and nickel concentrations as well as mechanisms of metal removal. The concentrations of bioavailable metal concentrations were determined after extraction with diethylene-triamine pentaacetate (DTPA)-extractable metals (Cd, Cr, Co, Cu, Pb, Mn, Ni, and Zn) from the soil samples by inductively coupled plasma-optical emission spectrometry (ICP-OES). Two indigenous T. harzianum strains were selected for copper tolerance, and three indigenous T. longibrachiatum strains were selected for nickel tolerance tests. Strains were isolated from the soils with the highest and among the lowest DTPA-extractable metal concentrations to determine whether the adaptation to different concentrations of metals affects the mechanisms of remediation. Mechanisms of metal removal were determined using Fourier-transform infrared spectroscopy (FTIR) and X-ray fluorescence spectroscopy (XRF), non-destructive methods characterized by high measurement speed with little or no need for sample preparation and very low costs. Increased DTPA-extractable metal content for nickel and copper was detected in the soil samples above the target value (TV), and for nickel above the soil remediation intervention values (SRIVs), for total metal concentrations which were previously determined. The SRIV is a threshold of metal concentrations indicating a serious soil contamination, thus confirming the need for soil remediation. The use of FTIR and XRF methods revealed that the presence of both biosorption and accumulation of metals in the Trichoderma cells, providing good bioremediation potential for Ni and Cu.

Ultrastructural evidences for chromium(III) immobilization by Escherichia coli K-12 depending on metal concentration and exposure time

Microorganisms can mediate in heavy metal sequestration through several cellular strategies and pathways. This offers an efficient way to remediate heavy metal polluted environments. This paper describes the ability of Escherichia coli K-12 to capture chromium(III) (Cr(III)) and the ultrastructural effects of this metal on cells, as well as the cellular metal localization and the possible sequestration strategy uses for it. The study was mainly performed by using several electron microscopy techniques and is based on the chromium trivalent concentration and the related exposure time. Transmission electron microscopy (TEM) assay was performed along with field emission scanning electron microscopy (FESEM) for morphological responses. Furthermore, TEM was coupled with an energy dispersive X-ray (TEM-EDX) and TEM with selected area electron diffraction (TEM-SAED) to conduct analytical assays. The exposed cultures to 10 and 12 mM Cr(III) at 12 h and to 5, 7, 10, 12, 13, and 15 mM of Cr(III) at 24 h indicated the presence of multiple electrodense granules that were significantly enriched in chromium and phosphorus content via EDX analysis. Moreover, these granules were observed to be attached to external membrane and/or surrounding cells in the respective ultrathin sections analyzed under TEM. According to these results, E. coli K-12 possesses the ability to immobilize Cr(III) in external polyphosphate granules through a strategy of accumulation, where cell response to Cr(III) toxicity seems to have a dose-dependent and time-dependent relation, thereby offering significant potential for bioremediation in Cr(III)-contaminated areas.

Cellular strategies against metal exposure and metal localization patterns linked to phosphorus pathways in Ochrobactrum anthropi DE2010

Cytotoxic, chemical, biochemical, compositional, and morphometric responses were analyzed against heavy metal exposure in Ochrobactrum anthropi DE2010, an heterotrophic bacterium isolated from Ebro Delta microbial mats (Tarragona, NE Spain). Several parameters of effect and exposure were evaluated to determine tolerance to a range of cadmium (Cd), lead (Pb(II)), copper (Cu(II)), chromium (Cr(III)), and zinc (Zn) concentrations. Additionally, removal efficiency, polyphosphate production and metal localization patterns were also analyzed. O. anthropi DE2010 showed high resistance to the tested metals, supporting concentrations of up to 20 mM for Zn and 10 mM for the rest of the elements. The bacterium also demonstrated a high removal capacity of metals-up to 90 % and 40 % for Pb(II) and Cr(III), respectively. Moreover, polyphosphate production was strongly correlated with heavy metal concentration, and three clear cell localization patterns of metals were evidenced using compositional and imaging techniques: (i) extracellular in polyphosphate granules for Cu(II); (ii) in periplasmic space forming crystals with phosphorus for Pb(II); and (iii) intracytoplasmic in polyphosphate inclusions for Pb(II), Cr(III), and Zn. The high resistance and metal sequestration capacity of O. anthropi DE2010 both highlight its great potential for bioremediation strategies, especially in Pb and Cr polluted areas.

Processing of Metals and Metalloids by Actinobacteria: Cell Resistance Mechanisms and Synthesis of Metal(loid)-Based Nanostructures

Metal(loid)s have a dual biological role as micronutrients and stress agents. A few geochemical and natural processes can cause their release in the environment, although most metal-contaminated sites derive from anthropogenic activities. Actinobacteria include high GC bacteria that inhabit a wide range of terrestrial and aquatic ecological niches, where they play essential roles in recycling or transforming organic and inorganic substances. The metal(loid) tolerance and/or resistance of several members of this phylum rely on mechanisms such as biosorption and extracellular sequestration by siderophores and extracellular polymeric substances (EPS), bioaccumulation, biotransformation, and metal efflux processes, which overall contribute to maintaining metal homeostasis. Considering the bioprocessing potential of metal(loid)s by Actinobacteria, the development of bioremediation strategies to reclaim metal-contaminated environments has gained scientific and economic interests. Moreover, the ability of Actinobacteria to produce nanoscale materials with intriguing physical-chemical and biological properties emphasizes the technological value of these biotic approaches. Given these premises, this review summarizes the strategies used by Actinobacteria to cope with metal(loid) toxicity and their undoubted role in bioremediation and bionanotechnology fields.

Effects of typical flotation reagent on microbial toxicity and nickel bioavailability in soil

The combined toxicological effects of nickel (Ni) and butyl xanthate (BX), that is commonly used in flotation reagents for non-ferrous metals ore processing such as Ni, copper and lead ores, on soil microbial communities were studied by determining soil microbial activity, soil enzyme activities and Ni bioavailability. The results revealed that the exchangeable (EXC) and reducible (RED) fractions of Ni were higher in Ni/BX mixture than Ni alone, probably because BX reacts with Ni to form complexes that lead an increase in bioavailability of Ni. The presence of BX and Ni inhibited microbial activity and enzyme activities during the first 30-days. Then, from 30 days to 180 days, different trends were observed according to the condition: microbial activity was stimulated with BX alone while it was inhibited with Ni/BX mixture. This observation was supported by the fact that the inhibitory ratio (I) was higher for Ni/BX mixture than BX alone. Results showed that the sensitivity to one or both contaminants followed the order: urease (UA) > invertase (INV). EXC fraction of Ni/BX mixture were significantly correlated with UA, INV, I, peak power (P_peak) and peak time (T_peak), respectively (p < 0.01), suggesting that Ni bioavailability might explain the Ni toxicity against microbial communities under combined pollution conditions. Such observations allow us to better understand toxic effects of Ni pollution when accompanied with BX, facilitating precisely evaluation of potential risks in mining areas.

Multi-approach analysis to assess the chromium(III) immobilization by Ochrobactrum anthropi DE2010

Ochrobactrum anthropi DE2010 is a microorganism isolated from Ebro Delta microbial mats and able to resist high doses of chromium(III) due to its capacity to tolerate, absorb and accumulate this metal. The effect of this pollutant on O. anthropi DE2010 has been studied assessing changes in viability and biomass, sorption yields and removal efficiencies. Furthermore, and for the first time, its capacity for immobilizing Cr(III) from culture media was tested by a combination of High Angle Annular Dark Field (HAADF) Scanning Transmission Electron Microscopy (STEM) imaging coupled to Energy Dispersive X-ray spectroscopy (EDX). The results showed that O. anthropi DE2010 was grown optimally at 0-2 mM Cr(III). On the other hand, from 2 to 10 mM Cr(III) microbial plate counts, growth rates, cell viability, and biomass decreased while extracellular polymeric substances (EPS) production increases. Furthermore, this bacterium had a great ability to remove Cr(III) at 10 mM (q = 950.00 mg g^-1) immobilizing it mostly in bright polyphosphate inclusions and secondarily on the cellular surface at the EPS level. Based on these results, O. anthropi DE2010 could be considered as a potential agent for bioremediation in Cr(III) contaminated environments.

Copper oxide nanoparticles as an effective anti-biofilm agent against a copper tolerant marine bacterium, Staphylococcus lentus

Biofilm formation on antifouling coatings is a serious concern in seawater cooling systems and the maritime industry. A prolific biofilm forming strain (Staphylococcus lentus), possessing high tolerance (>1,000 µg ml^-1) to dissolved copper ions (Cu⁺⁺) was isolated from titanium coupons exposed in the coastal waters of Kalpakkam, east coast of India. S. lentus formed increased biofilm (p < 0.05) at 100 µg ml^-1 of Cu⁺⁺ ions, when compared with the untreated control. To combat biofilm formation of this strain, the efficacy of copper oxide nanoparticles synthesized from copper nitrate by varying the concentrations of hexamine and cetyl trimethyl ammonium bromide (CTAB), was investigated. Complete (100%) inhibition of biofilm formation was observed with plain CuO NP (0.5 M hexamine, uncapped) at 1,000 µg ml^-1. Capping with CTAB, influenced the morphology and the purity of the synthesized CuO NPs but did not alter their surface charge. Capping reduced metal ion release from CuO NPs and their antibacterial and anti-biofilm property against S. lentus. Overall, uncapped CuO NPs were effective in controlling biofilm formation of S. lentus. Concurrent release of copper ions and contact mediated physical damage by CuO NPs offer a promising approach to tackle metal tolerant biofilm bacteria.

Active and passive biosorption of Pb(II)using live and dead biomass of marine bacterium Bacillus xiamenensis PbRPSD202: Kinetics and isotherm studies

A highly lead(II) resistant (up to 2200 mg/l) bacterium PbRPSD202 was selected among 210 lead resistant bacteria isolated from marine environment of Paradeep Port, Odisha for possible biosoption of toxic Pb (II) ions from metals polluted environments. The bacterium was identified as Bacillus xiamenensis following the phenotypic as well as 16S rRNA gene sequence analysis. In addition to Pb(II), it also showed resistance towards other heavy metals like Cd(II), Cr(VI), As(III), Cu(II), Ni(II) and Zn(II). Batch biosorption of Pb(II) using both live and dead biomass of this strain was investigated under different operational parametric conditions such as pH, temperature, NaCl concentration, shaking speed, treatment time, biomass concentration and initial Pb(II) concentration. The maximum Pb(II) uptake of 216.75 and 207.4 mg/g biomass was obtained with live and dead biomass, respectively, at the optimum condition (4% w/v NaCl, pH 6.0, 35 °C, 140 rpm and 1 g/l biosorbent dose). Both active as well as passive Pb(II) bio-sorption process showed best fit with the pseudo-second-order kinetic model. The sorption mechanism was favoured with Langmuir isotherm model indicating monolayer type adsorption. FTIR and FESEM-EDX analysis further ensured the possible interactions of Pb(II) with bacterial cell surface ligands like hydroxyl, carbonyl, carboxyl and amine groups during surface adsorption. TEM analysis revealed the intracellular accumulation of lead ions. This investigation highlights the potential application of this bacterium for bioremediation of lead(II) from the multiple metals contaminated saline environment through biosorption.

Combined Confocal Laser Scanning Microscopy Techniques for A Rapid Assessment of the Effect and Cell Viability of Scenedesmus sp. DE2009 Under Metal Stress

Phototrophic microorganisms are the dominant populations in microbial mats, which play an important role in stabilizing sediments, such as happens in the Ebro Delta. These microorganisms are exposed to low metal concentrations over a long period of time. Distinct methods have been used to evaluate their toxic effect on the preservation of these ecosystems. Nevertheless, most of these techniques are difficult to apply in isolated phototrophs because (i) they usually form consortia with heterotrophic bacteria, (ii) are difficult to obtain in axenic cultures, and (iii) do not grow on solid media.In this study, and for the first time, a combination of fast, non-invasive, and in vivo Confocal Laser Scanning Microscopy (CLSM) techniques were applied in a consortium of Scenedesmus sp. DE2009 to analyze its physiological state and viability under metal stress conditions. Microalga was more resistant to Pb followed by Cr and Cu. However, in multimetal combinations, the presence of Cu negatively affected microalga growth. Additionally, the inhibitory concentration (IC) values were also calculated by CLSM pigment analysis. The result determines a higher degree of toxicity for Cu and Cr in comparison to Pb. The high sensitivity of these CLSM-methods to detect low concentrations allows consideration of Scenedesmus sp. DE2009 as a good bioindicator of metal pollution in natural environments.

Morphological responses to nitrogen stress deficiency of a new heterotrophic isolated strain of Ebro Delta microbial mats

Microorganisms living in hypersaline microbial mats frequently form consortia under stressful and changing environmental conditions. In this paper, the heterotrophic strain DE2010 from a microalgae consortium (Scenedesmus sp. DE2009) from Ebro Delta microbial mats has been phenotypically and genotypically characterized and identified. In addition, changes in the morphology and biomass of this bacterium in response to nitrogen deficiency stress have been evaluated by correlative light and electron microscopy (CLEM) combining differential interference contrast (DIC) microscopy and transmission electron microscopy (TEM) and scanning electron microscopy (SEM). These isolated bacteria are chemoorganoheterotrophic, gram-negative, and strictly aerobic bacteria that use a variety of amino acids, organic acids, and carbohydrates as carbon and energy sources, and they grow optimally at 27 °C in a pH range of 5 to 9 and tolerate salinity from 0 to 70‰ NaCl. The DNA-sequencing analysis of the 16S rRNA and nudC and fixH genes and the metabolic characterization highlight that strain DE2010 corresponds to the species Ochrobactrum anthropi. Cells are rod shaped, 1-3 μm in length, and 0.5 μm wide, but under deprived nitrogen conditions, cells are less abundant and become more round, reducing their length and area and, consequently, their biomass. An increase in the number of pleomorphic cells is observed in cultures grown without nitrogen using different optical and electron microscopy techniques. In addition, the amplification of the fixH gene confirms that Ochrobactrum anthropi DE2010 has the capacity to fix nitrogen, overcoming N₂-limiting conditions through a nifH-independent mechanism that is still unidentified.

Soil bacterial communities of Sahara and Gibson deserts: Physiological and taxonomical characteristics

The purpose of this research was to investigate the structure of soil bacteria communities present in the Gibson (Australia) and the Sahara (Egypt) deserts, as well as to estimate strain survivability under different environmental factors. It should be noticed that the screening of bacterial resistance to wide spectra of principally different stress conditions was performed for the first time. Experiments were conducted with culturable bacterial communities. Strains were identified using 16S rRNA sequencing, and stress-tolerance was estimated by growing strains in various nutrient media. In order to characterize the community the epifluorescent microscopy and multisubstrate testing were also performed. High bacterial abundance in the desert soils was detected, and there was seen a significant proportion of culturable cells. The close numbers of psychotropic and mesophilic bacteria in arid ecosystems were revealed. The representatives of the Actinobacteria phylum were dominant in the microbial communities, and Firmicutes, Proteobacteria, and Bacteroidetes phyla representatives were also identified. Tolerance of the axenic bacterial cultures, isolated from arid desert ecotopes, to temperature, pH, salts (KCl, NaCl, MgSO4, NaHCO3), strong oxidizers (Mg(ClO4)2), and antibiotics (ampicillin, cephalexin, chloramphenicol, tetracycline, doxycycline, kanamycin, rifampicin) was studied. The bacterial isolates were characterized by polyextremotolerance and by the ability to maintain metabolic activity in vitro while influenced by a wide range of physicochemical and biotic factors.

Microcalorimetry and enzyme activity to determine the effect of nickel and sodium butyl xanthate on soil microbial community

In non-ferrous metal tailings, combined pollution in the surrounding soil is caused by heavy metals and flotation chemicals. The combined effects of nickel (Ni) and its primary ore processing collector, sodium butyl xanthate (SBX), on soil microbial activity were investigated following the fluorescein diacetate hydrolase (FDA) and sucrase (SA) activities, and isothermal microcalorimetry during 60 days. FDA and SA activities as well as overall soil microbial activity were significantly affected by Ni, SBX and Ni/SBX mixture. The inhibition rate (I) of the growth rate constant (k) being higher with the Ni/SBX mixture than with SBX alone during the experiment. The growth rate constant (k) was positively correlated (p < 0.05 or p < 0.01) with enzyme activities (FDA and SA) indicating that k represented a valuable proxy to evaluate the toxic effect of metals and flotation reagents on soil microorganisms. Thus, microcalorimetry was a useful method to characterize soil microbial communities.

A critical review on speciation, mobilization and toxicity of lead in soil-microbe-plant system and bioremediation strategies

Lead accumulation in soils is of serious concern in agricultural production due to the harmful effects on soil microflora, crop growth and food safety. In soil, speciation of lead greatly affects its bioavailability and thus its toxicity on plants and microbes. Many plants and bacteria have evolved to develop detoxification mechanisms to counter the toxic effect of lead. Factors influencing the lead speciation include soil pH, organic matter, presence of various amendments, clay minerals and presence of organic colloids and iron oxides. Unlike, other metals little is known about the speciation and mobility of lead in soil. This review focuses on the speciation of lead in soil, its mobility, toxicity, uptake and detoxification mechanisms in plants and bacteria and bioremediation strategies for remediation of lead contaminated repositories.

Microbial strategy for potential lead remediation: a review study

The extensive exploitation and usage of lead compounds result in severe lead(II) pollution in water and soil environments, even in agricultural land, threatening the health of animals and humans via food chains. The recovery and remediation of lead(II) from water and soil environments have been intensively concerned in recent years. Compared with the traditional physic-chemistry treatment, microbial remediation strategy is a promising alternative to remediate lead(II)-contaminated environments due to its cost-effective and environmentally-friendly properties. Various microorganisms are capable of removing or immobilizing lead(II) from water and soil environments through bioaccumulation, precipitation or accelerated transformation of lead(II) into a very stable mineral, resulting in significant effects on lead(II) mobility and bioavailability. In the present review, we investigated a wide diversity of lead(II) bioremediation induced by different microbes and its multi-mechanisms. Moreover, we also discussed the progress and limitations, summarized the common rules of lead(II)-microbe interaction, and evaluated the environmental significance of microbes in lead biogeochemistry process. In addition, we further deliberated the feasibility and potential application of microbes in developing cost-effective, eco-friendly bioremediation or long-term management strategy for lead(II) contaminated repositories.

Isolation and identification of Aeromonas caviae strain KS-1 as TBTC- and lead-resistant estuarine bacteria

Tributyltin chloride (TBTC)- and lead-resistant estuarine bacterium from Mandovi estuary, Goa, India was isolated and identified as Aeromonas caviae strain KS-1 based on biochemical characteristics and FAME analysis. It tolerates TBTC and lead up to 1.0 and 1.4 mM, respectively, in the minimal salt medium (MSM) supplemented with 0.4 % glucose. Scanning electron microscopy clearly revealed a unique morphological pattern in the form of long inter-connected chains of bacterial cells on exposure to 1 mM TBTC, whereas cells remained unaltered in presence of 1.4 mM Pb(NO₃)₂ but significant biosorption of lead (8 %) on the cell surface of this isolate was clearly revealed by scanning electron microscopy coupled with energy dispersive X-ray spectroscopy. SDS-PAGE analysis of whole-cell proteins of this lead-resistant isolate interestingly demonstrated three lead-induced proteins with molecular mass of 15.7, 16.9 and 32.4 kDa, respectively, when bacterial cells were grown under the stress of 1.4 mM Pb (NO₃)₂. This clearly demonstrated their possible involvement exclusively in lead resistance. A. caviae strain KS-1 also showed tolerance to several other heavy metals, viz. zinc, cadmium, copper and mercury. Therefore, we can employ this TBTC and lead-resistant bacterial isolate for lead bioremediation and also for biomonitoring TBTC from lead and TBTC contaminated environment.

The effect of copper on different phototrophic microorganisms determined in vivo and at cellular level by confocal laser microscopy

Microbial mats are coastal ecosystems that consist mainly of cyanobacteria, primary producers in these habitats that play an important role in stabilising delta sediments. However, these ecosystems are subject to various kinds of pollution, including metal contamination, placing their survival at risk. Among heavy metals, copper is an essential metal at low doses and toxic at high doses. This metal is present in different pesticides used in rice production, a thriving agro-industry in the Ebro Delta (Spain). For several years, our group has been studying the Ebro Delta microbial mats and has developed a method for determining the effect that metals cause on cyanobacteria populations. This method is based on confocal laser microscopy coupled to a spectrofluorometer, which rapidly provides simultaneous three-dimensional information on photosynthetic microorganisms and their fluorescence spectra profiles. The current study determines the copper effect on different photosynthetic microorganisms from culture collection (Chroococcus sp. PCC 9106 and Spirulina sp. PCC 6313) and isolated from the environment (Microcoleus-like and the microalga DE2009). Comparing all results obtained it can be observed that the minimum dose of Cu that is capable of significantly altering chlorophyll a (chl a) fluorescence intensity were 1 × 10(-7) M in Chroococcus sp. PCC 9106; 1 × 10(-7) M in Spirulina sp. PCC 6313; 3 × 10(-7) M in Microcoleus and 5 × 10(-6) M in the microalga DE2009. Moreover, the sensitivity of the technique used was 1 × 10(-7) M.

Biosorption of lead and copper by heavy-metal tolerant Micrococcus luteus DE2008

Micrococcus luteus DE2008 has the ability to absorb lead and copper. The effect of these metals on biomass and viability of this microorganism were investigated and removal of the metals from culture media was determined. Lead had no effect on the biomass expressed as mg Carbon/cm(3) of M. Iuteus DE2008, but in the case of copper, the minimum metal concentration that affected the biomass was 0.1 mM Cu(II). According to these results this microorganism shows a greater tolerance for lead. The minimum metal concentration that affected viability (expressed as the percentage of live cells) was 0.5 mM for both metals. M. luteus DE2008 exhibited a specific removal capacity of 408 mg/g for copper and 1965 mg/g for lead. This microorganism has a greater ability to absorb Pb(II) than Cu(II). M. luteus DE2008 could be seen as a microorganism capable of restoring environments polluted by lead and copper.

Sequestration and in vivo effect of lead on DE2009 microalga, using high-resolution microscopic techniques

Algae are primary producers in a wide variety of natural ecosystems, and these microorganisms have been used in bioremediation studies. Nevertheless, very little is known about the in vivo effect of heavy metals on individual living cells. In this paper, we have applied a method based on confocal laser scanning microscopy and lambda scan function (CLSM-λscan) to determine the effect of lead (Pb), at different concentrations, on the DE2009 microalga. At the same time, we have optimized a method based on CLSM and image-analysis software (CLSM-IA) to determine in vivo biomass of this microorganism. The results obtained by lambda scan function indicated that the pigment peak decreases while the concentration of metal increases at pH 7. On the other hand at pH 4 there is no good correlation between the concentration of metal and the intensity of the emission of fluorescence of the pigment. Also, in some cases a displacement of the Chl a peak towards 680 nm is produced. Total and individual biomass determined by CLSM-IA shows statistically significant differences between unpolluted and 10 mM polluted cultures. Complementary studies using electron microscopy techniques coupled to energy dispersive X-ray microanalysis (EDX) demonstrate that the microalga can sequestrate Pb extra- and intracellularly.